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- PDB-7raw: Domain 1 of Starch adherence system protein 20 (Sas20) from Rumin... -

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Basic information

Entry
Database: PDB / ID: 7raw
TitleDomain 1 of Starch adherence system protein 20 (Sas20) from Ruminococcus bromii
ComponentsDockerin domain-containing protein
KeywordsSUGAR BINDING PROTEIN / Starch-binding protein domain in the Ruminococcus bromii amylosome protein Sas20
Function / homology
Function and homology information


cellulose catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds
Similarity search - Function
Dockerin domain / Dockerin domain profile. / Dockerin type I domain / Dockerin type I repeat / Dockerin domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Dockerin domain-containing protein
Similarity search - Component
Biological speciesRuminococcus bromii L2-63 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsCerqueira, F.M. / Koropatkin, N.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F31 GM137488 United States
CitationJournal: J.Biol.Chem. / Year: 2022
Title: Sas20 is a highly flexible starch-binding protein in the Ruminococcus bromii cell-surface amylosome.
Authors: Cerqueira, F.M. / Photenhauer, A.L. / Doden, H.L. / Brown, A.N. / Abdel-Hamid, A.M. / Morais, S. / Bayer, E.A. / Wawrzak, Z. / Cann, I. / Ridlon, J.M. / Hopkins, J.B. / Koropatkin, N.M.
History
DepositionJul 4, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2022Provider: repository / Type: Initial release
Revision 1.1May 25, 2022Group: Database references / Category: citation / citation_author / Item: _citation.journal_volume / _citation_author.name
Revision 1.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dockerin domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7813
Polymers27,5241
Non-polymers2562
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)130.032, 130.032, 130.032
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number199
Space group name H-MI213
Components on special symmetry positions
IDModelComponents
11A-490-

HOH

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Components

#1: Protein Dockerin domain-containing protein


Mass: 27524.311 Da / Num. of mol.: 1 / Fragment: Domain 1 of Doc20
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruminococcus bromii L2-63 (bacteria) / Strain: L2-63 / Gene: RBL236_01231 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2N0URA4
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.54 Å3/Da / Density % sol: 65.3 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.024M 1,6-Hexanediol; 0.024M 1-Butanol 0.024M 1,2-Propanediol; 0.024M 2-Propanol; 0.024M 1,4-Butanediol; 0.024M 1,3-Propanediol; 0.1M Imidazole; 0.1M MES monohydrate; 20% PEG 500 MME; 10% PEG 20000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.979 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jun 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.099→41.12 Å / Num. obs: 21541 / % possible obs: 100 % / Redundancy: 14.8 % / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.019 / Rrim(I) all: 0.074 / Χ2: 0.977 / Net I/σ(I): 8.7
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2
2.1-2.14132.31110510.4310.6652.4060.885
2.14-2.1814.11.98810560.5610.5482.0620.882
2.18-2.22151.61310780.6990.431.670.865
2.22-2.26151.39110690.7720.3711.440.869
2.26-2.3115.11.19610630.8150.3181.2370.866
2.31-2.37151.00510640.8530.2681.0410.88
2.37-2.42150.83510760.8880.2220.8640.864
2.42-2.4915.10.65710630.9340.1750.680.877
2.49-2.5615.10.5210800.9620.1380.5380.891
2.56-2.6515.10.4210610.9690.1110.4340.881
2.65-2.7415.10.29310730.9820.0780.3030.921
2.74-2.8515.10.22310690.990.0590.2310.945
2.85-2.98150.15510920.9950.0410.161.017
2.98-3.1415.10.10910610.9960.0290.1131.111
3.14-3.33150.08310730.9980.0220.0861.114
3.33-3.59150.06810870.9980.0180.071.259
3.59-3.9514.90.05910810.9990.0160.0611.343
3.95-4.5214.90.0511050.9990.0130.0521.291
4.52-5.6914.80.04110990.9990.0110.0421.027
5.69-3014.10.03211400.9990.0090.0330.712

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→30 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2142 1995 9.27 %
Rwork0.1768 19527 -
obs0.1802 21522 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 155.61 Å2 / Biso mean: 65.7003 Å2 / Biso min: 27.98 Å2
Refinement stepCycle: final / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1793 0 41 111 1945
Biso mean--98.82 55.98 -
Num. residues----235
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.1-2.15140.32421440.28111388
2.1514-2.20960.28111420.24251385
2.2096-2.27460.29561360.22531359
2.2746-2.3480.24431410.21741382
2.348-2.43190.26421420.21561380
2.4319-2.52930.22961440.19831388
2.5293-2.64440.23941380.20111380
2.6444-2.78380.2071450.19831395
2.7838-2.95810.31081400.20531405
2.9581-3.18640.28271420.19891388
3.1864-3.50690.22731420.19831388
3.5069-4.0140.19971410.16321410
4.014-5.05580.17551460.13961418
5.0558-300.16511520.15141461
Refinement TLS params.Method: refined / Origin x: -4.1371 Å / Origin y: 10.2686 Å / Origin z: -21.3276 Å
111213212223313233
T0.4595 Å2-0.0711 Å2-0.0449 Å2-0.2946 Å20.036 Å2--0.3962 Å2
L2.6012 °2-0.6374 °2-0.012 °2-3.8273 °2-1.2922 °2--1.9236 °2
S0.0344 Å °-0.0933 Å °0.2914 Å °0.3997 Å °-0.1786 Å °-0.518 Å °-0.526 Å °0.2829 Å °0.0735 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA3 - 237
2X-RAY DIFFRACTION1allA301 - 401
3X-RAY DIFFRACTION1allS1 - 138

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